Data

Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis

Conlon, B.H., Gostinčar, C., Fricke, J., Kreuzenbeck, N., Daniel, J.-M., Schlosser, M.S.L., Peereboom, N. Aanen, D.K., De Beer, Z.W., Beemelmanns, C., Gunde-Cimerman, N., Poulsen, M. (2021). Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis. iScience 24, 102680
ITS sequence data, NCBI – GenBank: MW430027-MW430047
Whole-genome sequence data NCBI – BioProject: PRJNA681736

You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts

Bos, N., Guimaraes, L., Palenzuela, R. et alBMC Evol Biol 20, 163 (2020). https://doi.org/10.1186/s12862-020-01727-z

Data

  • MiSeq amplicon sequences, BioProject
  • DNA sequences: GenBank accessions MT887350—MT887596.

Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly

Justinn Renelies-Hamilton, Kristjan Germer, David Sillam-Dussès, Kasun H. Bodawatta, Michael Poulsen. mSphere Jan 2021, 6 (1) e01023-20; https://doi.org/10.1128/mSphere.01023-20

SRA data: BioProject PRJNA642018

Other supplementary data: https://zenodo.org/record/4074900 with DOI 10.5281/zenodo.4074900

Disease-free monoculture farming by fungus-growing termites

Otani, S., Challinor, V.L., Kreuzenbeck, N.B. et al. Sci Rep 9, 8819 (2019). https://doi.org/10.1038/s41598-019-45364-z

 

Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community

Hu H, da Costa RR, Pilgaard B, Schiøtt M, Lange L, Poulsen M. mSphere. 2019 May 15;4(3):e00165-19. DOI: 10.1128/mSphere.00165-19

  • Clean reads and metagenome assembly have been submitted to the SRA and GenBank under BioProject accession numbers PRJNA476694 and PRJNA193472.

 

Complementary symbiont contributions to plant decomposition in a fungus-farming termite

Poulsen, M., Hu, H., Li, C., Chen, Z., Xu, L., Otani, S., … Zhang, G. (2014). Proceedings of the National Academy of Sciences, 111(40), 14500–14505. doi:10.1073/pnas.1319718111

Datasets: http://gigadb.org/dataset/100055

 

Comparative genomic and metabolic analysis of Streptomyces sp. RB110 morphotypes illuminates genomic rearrangements and formation of a new 46-membered antimicrobial macrolide

Um, S., Rischer, M., Murphy, R., Benndorf, R., Braga, D., Poulsen, M. Lackner, G., and Beemelmanns, C. (2021). ACS Chemical Biology, https://doi.org/10.1021/acschembio.1c00357

Genomes accession numbers RB110−1: JAEKDS000000000.1 and RB110−2: JAEKDR000000000.1.

The termite fungal cultivar Termitomyces combines diverse enzymes and oxidative reactions for plant biomass conversion

Schalk, F., Gostinčar, C., Kreuzenbeck, N., Conlon, B.H., Sommerwerk, E., Rabe, P., Burkhardt, I., Krüger, T., Kniemeyer, O., Brakhage, A.A., Gunde-Cimerman, N., de Beer, Z.W., Dickschat, J., Poulsen, M. and Beemelmanns, C. (2021). mBio 12, e03551-20. https://doi.org/10.1128/mBio.03551-20  
Redox, CAZy and proteomics analyses available from zenodo via https://zenodo.org/record/4781753#.YRYhCO2xXdc 

Comparative genomics reveals prophylactic and catabolic capabilities of Actinobacteria within the fungus-farming termite symbiosis

Murphy, R. Benndorf, R., de Beer, Z.W., Vollmers, J., Beemelmanns, C., and Poulsen, M. (2021). mSphere 6, e01233-20. https://doi.org/10.1128/mSphere.01233-20 
RB22, RB24, RB33, and RB110 assemblies and annotated GenBank files were deposited to Zenodo (https://doi.org/10.5281/zenodo.4302144).

Streptomyces smaragdinus sp. nov. isolated from the gut of the fungus-growing termite Macrotermes natalensis

Schwitalla, J.W., Benndorf, R., Martin, K., Vollmers, J., Kaster, A.-K., de Beer, Z.W., Poulsen, M. and Beemelmanns, C. International Journal of Systematic and Evolutionary Microbiology https://doi.org/10.1099/ijsem.0.004478 
The GenBank/EMBL accession number for the partial 16S rRNA gene sequence of strain RB5T is KY558696.2. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession WEGJ00000000. The version described in this paper is WEGJ01000000.1.

Nocardia macrotermitis sp. nov. and Nocardia aurantia sp. nov., isolated from the gut of the fungus-growing termite Macrotermes natalensis

Benndorf, R., Schwitalla, J.W., Martin, K., de Beer, Z.W., Vollmers, J., Kaster, A.-K., Poulsen, M., and Beemelmanns, C. International Journal of Systematic and Evolutionary Microbiology https://doi.org/10.1099/ijsem.0.004398 
The GenBank/EMBL accession numbers for the partial 16S rRNA gene sequences of strains RB20T and RB56T are KY558706.2 and KY558730.2, respectively. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accessions WEGK00000000.1 and WEGI00000000.1, respectively. The versions described in this paper are version WEGK01000000.1 and WEGI01000000.1, respectively

Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerine birds are shaped by diet and flight-associated gut modifications

Bodawatta, K. H., Koane, B., Maiah, G., Sam, K. Poulsen, M and Jønsson, K. A. (2021). Proceedings of the Royal Society B 288: 20210446, https://doi.org/10.1098/rspb.2021.0446.
Microbiome data is available from the GenBank SRA archive (PRJNA673614, PRJNA673602, PRJNA673580, PRJNA673591).

The gut microbiota of Parus major (Great Tits) flexibly responds to macronutrient dietary contents

Bodawatta, K. H., Freiberga, I., Puzejova, K., Sam, K., Poulsen, M., and Jønsson, K. A. (2021). BMC Animal Microbiome 3:20, https://doi.org/10.1186/s42523-021-00076-6.
Microbiome data is available from the GenBank SRA database (PRJNA548757).

Great tit (Parus major) uropygial gland microbiomes and their potential defensive roles.

Bodawatta, K. H., Schierbech, S. K., Petersen, N. R., Bos, N., Jønsson, K.A. and Poulsen, M. (2020). Frontiers in Microbiology 11: 1735, https://doi.org/10.3389/fmicb.2020.01735.
Microbiome data is available from the GenBank SRA database (SAMN14479100–SAMN14479109) and bacterial Sanger sequences are available in GenBank (MT276619–MT276666).

Spatiotemporal patterns of avian host-parasite interactions in the face of biogeographical range expansions

Bodawatta, K. H., Synek, P., Bos, N., Garcia-del-Rey, E., Koane, B., Marki, P. Z., Albrecht, T., Lifjeld, J., Poulsen, M., Munclinger, P., Sam, K., and Jønsson, K. A. (2020). Molecular Ecology 19: 2431 – 2448, https://doi.org/10.1111/mec.15486
Haemosporidian sequences are available on GenBank under accessions MK061561–MK061743.

Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

Bodawatta, K. H., Puzejova, K. Sam, K., Poulsen, M., and Jønsson, K. A. (2020). BMC Animal Microbiome 2: 9, https://doi.org/10.1186/s42523-020-00026-8.
Microbiome data is available from the GenBank SRA database (PRJNA591550, SAMN13383021 – SAMN13383134, SRR9295628, SRR9295605, SRR9295561,SRR9295668, SRR9295635, SRR9295590, SRR9295610, SRR9295576, SRR9295676, SRR9295651, SRR9295639, SRR9295585).

Gut microbial compositions mirror caste‐specific diets in a major lineage of social insects

Otani, S., Zhukova, M., Koné, N.A., da Costa, R.R., Mikaelyan, A., Sapountzis, P. and Poulsen, M. (2019), Environmental Microbiology Reports, 11: 196-205. https://doi.org/10.1111/1758-2229.12728

  • Clean reads are submitted to GenBank, where sample sequences with their accession numbers are under a single SRA submission with the accession SRP144287

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